FUNDAMENTALS I: 10:00 – 11:00
FRIDAY, OCTOBER 1, 2010
BARNUM
FINAL IMMUNOLOGY OVERVIEW
Scribe: RACHEL TUCKER
Proof: BO BRADFORD
Page 1 of 5
Goal of today’s lecture
 walk you through a bacterial or viral infection in terms of innate and adaptive immune responses, bringing into that
scenario the players that you’ve seen so far in the lectures.
Scenario
 You’re in lab and one of your lab mates goes to a Petri dish full of bacteria, fills up a loop and flicks it at your face
(whiskey tango foxtrot, dude). Some of it gets in your nose, your mouth, a cut on your face. This is the scenario
for a bacterial infection.
 You won’t die from this unless it’s something like a Methicillin resistant strain.
The innate immune response
 So you have bacteria, with some of it on your skin, some in your mouth and nose
o In your mouth or nose, that’s the mucosal immune system.
o If it hits your skin, and the skin is intact, not much will happen. This is the first line barrier of the innate
immune defense system. It prevents the bacteria from even getting in.
 It blocks infection
 It has a slightly lower pH than neutral, which will be at least bacteriostatic. Bacteria won’t die but
they won’t reproduce well.
 Defensins are present: natural antibiotics produced by a variety of different cell types in the body.
 Normal flora is present: competes with what has been flicked onto your face so that it can’t set up
shop. There will be competition for resources, temperature, and places to stay.
 If you have a cut in your skin, the barrier is not intact and the bacteria will be happier.
o No competition with other bacteria because your tissues should be sterile; warm, plenty of fluids for food
supply
 In terms of innate immune responses, however, several cell types will be in skin.
o Mast cells and macrophages
o Neutrophils will not be present. They’re mostly in the blood. Neutrophils in the skin are a tell tale sign of
infection and they’ve been recruited into that site.
o Antigen presenting cells (APCs) are present here. In the skin, these are Langerhan’s cells.
 Macrophages will encounter the bacteria and recognize them via pathogen associated molecular patterns
(PAMPs): LPS, flagellin, peptidoglycan
o This is how the innate immune system sees bacteria.
o Toll like receptors, for example, are pattern recognition receptors that bind to the PAMPs. They’re on the
surface of lots of different cells of the immune system.
 LPS on the surface of the bacterium will also activate complement.
o The complement system can coat the bacterium in complement fragments.
o Macrophages have receptors for these complement components, which help the macrophage
phagocytize and internalize that bacterium to help get rid of it.
o Depending on the type of bacteria, the complement system may also be able to directly lyse it and kill it.
o Complement can also serve as a chemoattractant to bring in neutrophils, more macrophages.
 The macrophage, when it encounters bacteria through its pattern receptors, will produce proinflammatory
cytokines.
o This will further activate the macrophages.
o Will also activate mast cells (complement components like C5a will do this as well).
 Activated mast cells will degranulate. They may release:
o preformed cytokines (e.g. TNF, a proinflammatory cytokine)
o histamine and other vasoactive amines
 This will increase vascular permeability in the area so that post capillary venules will become
leaky.
 This will make it easier for neutrophils to leave the blood and go to the site of infection.
 Serum components may also enter the tissue, including perhaps some antibody (Ab) if you’ve
encountered the pathogen before. These Ab will bind the bacteria and make phagocytosis easier
for macrophages and invading neutrophils.
 Neutrophils also make defensins and are especially good at killing invading pathogens by phagocytosis.
o When bacteria are phagocytized, they are put inside a vesicle.
FUNDAMENTALS I: 10:00 – 11:00
FRIDAY, OCTOBER 1, 2010
BARNUM
FINAL IMMUNOLOGY OVERVIEW
Scribe: RACHEL TUCKER
Proof: BO BRADFORD
Page 2 of 5
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The vesicle then fuses with other vesicles that are loaded with granules that have proteolytic enzymes, as
well as enzymes that will chew up carbohydrates, lipids, or any other subcellular component that is found
in an invading pathogen.
o They can also make free radicals: superoxide anion, hydrogen peroxide
o They also make bleach (HOCl)
 During WWI we started to realize how effective bleach is at killing pathogens. A material called
Dakin’s solution (dilute bleach) was named after a British doctor, who discovered that soldiers’
gangrenous wounds could be treated by pouring dilute bleach solution on them to kill off all the
bacteria. It didn’t feel good, but saved a few legs and arms.
So, just from the innate point of view, it’s amazing that you ever get infected. There are so many different
components; we haven’t even covered everything. There are many different cell types that produce inflammatory
mediators in order to directly kill a pathogen, or alert cell types that can come in and do the killing.
o Macrophages can also phagocytize and kill.
o Neutrophils have a recently characterized, funky property: they make neutrophil extracellular traps (NETs)
 Neutrophils die pretty quickly anyway, but they can have their receptors tweaked to initiate
formation of NETs.
 They disassemble all chromatin into loose fibers and then blow their guts out into the surrounding
area.
 Chromatin is bacteriocidal, so this is another way to kill any bacteria in the area.
 Enzymes are also associated with this chromatin that will help degrade the pathogen.
Connecting to the adaptive immune response
 In many cases the innate immune response can take care of infections and it is not necessary to involve the
adaptive response.
 However, the best immune response will be when both systems are present and working.
o If you encounter the pathogen a second time, you’ll have a second powerful arsenal to take care of that
invading pathogen, in addition to the innate response.
o We talk about the two systems separately because it’s easier to compartmentalize them and describe
them that way, but they work together all the time.
 Langerhan’s cells don’t do very much in the way of killing, but are antigen presenters.
o They will pick up the antigen and will start the process of antigen presentation.
 Macrophages can also present antigen.
 B cells are great at presenting antigen. They can directly interact with T cells to activate the adaptive immune
response.
 Audio skips here.
Mucosal immune response
 The barriers for the mucosal immune response are saliva, tears, mucous.
o These serve to prevent invading pathogens from staying inside of you.
o Saliva will be swallowed and will end up in the stomach, where the pH is low and enzymes will degrade
the pathogens.
o Tears will try to wash things away. Tears also have antibodies and lysozyme (chews up bacterial cell
wall), probably defensins as well.
o The entire mucosal system is lined with mucous. This will prevent the pathogens from getting further in
and setting up shop.
 If the pathogens manage to get past the mucosal layer, then they will encounter the epithelial cell layer, which
they must attach to or breach. If they cannot do this, they will wither and die because they can’t survive in the
environment there.
 If you survive the stomach, the small intestine is next.
o This is an immediate shift to a higher pH, with bile salts and defensins and other enzymes that will attack
invading pathogens.
 If it makes it to the large intestine:
o Normal flora, billions and billions of bacteria, are present, so the pathogen cannot easily set up shop.
Some can do this, but not all. It depends on the route that they take to attempt to cause an infection.
 Ultimately, pathogens will be expelled.
 The mucosa try to prevent things from breaching that barrier in the first place and then molecules and enzymes
are present to degrade pathogens and prevent them from causing an infection.
FUNDAMENTALS I: 10:00 – 11:00
FRIDAY, OCTOBER 1, 2010
BARNUM
FINAL IMMUNOLOGY OVERVIEW
Scribe: RACHEL TUCKER
Proof: BO BRADFORD
Page 3 of 5
Deficiencies in the innate immune system
 What happens if you’re deficient in any one of these components? You’ll have lots of problems.
o Deficiencies in any component of the complement system.
o Defects in phagocytic cells, where they can’t make reactive oxygen species.
o Cytokine deficiencies are not very common, but possible.
o Realize that if you miss that first line of defense, you’ll be very susceptible to infections and in some
cases there’s not very much that can be done. They’ll live on antibiotics their entire lives and will have
serious problems as a result of their defect.
Questions about the innate immune response
 How closely are PAMPs associated with the term epitope?
Not really, because an epitope is a 3D structure that an Ab will recognize. This is specific immunity; an Ab has
been designed just to recognize that and that alone. A PAMP is broad spectrum. It allows 12 or 13 different TLRs
to recognize hundreds and hundreds of types of bacteria that may, for example, have LPS or peptidoglycan in
their cell wall even though they’re very diverse in nature. There is a big difference between PAMPs and epitopes.
 Where do the natural killer cells (NK cells) come in?
NK cells are more involved in viral infections. Their job is to patrol the body looking to see if cells have MHC class
I molecules on the surface and that they’re expressing activation receptors. They’re still considered part of the
innate immune system. There’s no gene rearrangement or specialized receptors like Ab or T cell receptors
(TCRs) on them. Their job is to control viral infections. This will be covered more in Ag presentation.
The adaptive immune response
 The innate immune response is present all the time and works immediately as soon as it encounters a pathogen.
It doesn’t have any memory, so the next time it encounters that pathogen it won’t work faster, better, or more
vigorously than it did the first time. It doesn’t recognize the pathogen in a horrifically specific way other than
through pattern receptor molecules.
 The adaptive immune response takes a little bit longer to occur, but has exquisite specificity in what it recognizes.
 It takes it longer to gear up because it has to find the right T cells and B cells that are specific for that particular
pathogen. There may only be 10 or 50 clones that recognize a particular bacterium or virus.
o This is why immune surveillance is constantly occurring.
o Trafficking of T and B cells through different lymph nodes throughout the body so that you have the best
chance of getting that particular T or B cell to the right spot to be able to interact with that given pathogen.
 When a pathogen is first encountered, APCs take the Ag to a site where you can have good Ag presentation and
get the adaptive immune response kicked off.
o Lymph node if it’s in the tissues
o Spleen if it’s in the blood
o Peyer’s patch if its in the mucosa
o These are the three sites where Ag processing and presentation occurs.
 When the Ag has been brought to the correct site, the Ag must interact with the proper T and B cells.
 When Ag is processed, it’s chewed up into tiny bits and peptides are presented.
o Endogenous pathway
 the pathogen is replicating intracellularly. Some of that material gets chewed up through the
proteosome.
 The proteosome normally turns over proteins that are no longer useful. When an infection occurs
and there’s inflammation and lots of cytokines produced, the cytokines cause the modification of
the proteosome so it has extra subunits which will specifically cut proteins into peptide sizes and
sequences that are very good for loading into MHC class I and class II molecules to be sent to
the surface for Ag presentation.
 Will load peptides into MHC class I
o Exogenous pathway
 The Ag has been phagocytized from outside the cell; Ag material is derived from phagocytosis.
 Will load peptides into MHC class II.
o Both MHC class I and MHC class II are made of two chains.
 Class I has one chain in the membrane and the other is 2 microglobulin
 Class II has two different peptides
 They can bind a range of peptides, but can bind only one peptide at a time.
FUNDAMENTALS I: 10:00 – 11:00
FRIDAY, OCTOBER 1, 2010
BARNUM
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FINAL IMMUNOLOGY OVERVIEW
Scribe: RACHEL TUCKER
Proof: BO BRADFORD
Page 4 of 5
Question: So a macrophage will encounter Ag in tissue or near the infection site and take it back to the lymph
node to present?
o Right. In the tissues, you don’t have a lot of T cells and B cells. You must get the Ag to the right site to get
T and B cells activated. The lymphatic system is the vascular system that is made of open ended vessels
in all the tissues. Fluid and also APCs can traffic through this way and go back to regional lymph nodes
near where the infection occurred.
At this point, Ag has been brought to the correct location and is being presented on an APC in order to interact
with T cells.
o CD8, or cytotoxic, T cells interact with MHC I. These T cells directly kill infected cells.
o CD4, or helper, T cells interact with MHC II.
The events that occur in any of the three sites where Ag is presented (spleen, lymph node, Peyer’s patch) are
relatively similar. There are some structural differences between the tissues.
The Peyer’s patch doesn’t have a capsule-type structure like the spleen and lymph node. It’s more a loose
aggregation of tissues.
o M (microvillus) cells in the dome of the Peyer’s patch is where Ag enters.
o Ag is taken further down into the Peyer’s patch, past M cells, where APCs, T cells, and B cells reside in a
loose aggregation.
o IgA is produced in this system.
o The mucosal system is also known as the common mucosal immune system. When B cells are stimulated
to make Ab will traffic to other mucosal sites. This allows for protection not only where the Ag was
encountered, but also throughout the mucosal immune system. (e.g. if the Ag is encountered in the
throat, protection will also be conferred to the nasal area)
o IgA is typically dimeric. It dimerizes using the J chain. This allows dimeric IgA to move out into mucosal
sites so it can interact with the pathogen and neutralize it so that it can be washed away by the mucosal
immune system.
In lymph node or in the spleen, there are germinal centers and zones of T cells and B cells.
A B cell encounters the Ag and recognizes it with its B cell receptor (i.e. surface immunoglobulin).
o On a B cell that is still naïve, this will be IgM.
When a B cell becomes activated, isotype switching may occur and another Ig isotype may be made.
o In isotype switching, it is the Fc region of Ab that changes. The variable region is retained; it doesn’t
change.
o It occurs by gene rearrangements of the heavy and light chains to give the Ab binding region of the
molecule.
When the B cell encounters its pathogen and recognizes it via its surface Ig, it will internalize the pathogen,
degrade it, and present it in MHC II in the form of a small peptide.
o This is the best scenario. The B cell specific for that pathogen is there; all that’s necessary is the T cell
that is also specific for that pathogen.
The T cell uses a TCR generated by gene rearrangements so that each T cell expresses a TCR with a single
specificity.
In the zones of the spleen and lymph node, T cells and B cells are initially kept separate. However, the zones are
dynamic. The cells are constantly moving around in these zones so that they have a better chance of interacting
with each other and finding the right T cell and B cell interaction.
Cognate recognition: when a T cell and B cell recognizing the same Ag come together.
o This leads to strong activation of both the B cell and the T cell.
o Signal 1: interaction of the TCR with the complex of MHC II and the pathogen derived pathogen.
o Signal 1 alone is not enough to activate the cells. With just this signal, the cells will become anergic or will
die.
o Signal 2: molecules like CD28 and B7 (found on B cells)
o The combination of these two very specific signals will activate the T cell and B cell to start producing
cytokines
o Cytokines will interact in a very localized area, just between these two cells.
o Autocrine production for the T cell of IL-2 is necessary.
o These cells exchange cytokines to turn each other on; the end result for both is the maturation process.
o At the time of cognate recognition, they’re both naïve cells.
The point of this entire recognition process:
o Make sure they’re on the same page in regards to the Ag.
o Get the cells to mature into effector cells to perform their specific function depending on the cell type.
FUNDAMENTALS I: 10:00 – 11:00
FRIDAY, OCTOBER 1, 2010
BARNUM
FINAL IMMUNOLOGY OVERVIEW
Scribe: RACHEL TUCKER
Proof: BO BRADFORD
Page 5 of 5
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Get the cells to proliferate a lot. If you start out with just 10 or 20 specific T or B cells, the response will
not be sufficient.
During cell expansion, some cells will become effector cells, some will become memory cells that will set up shop
elsewhere in the body.
o This way if the pathogen is encountered a second time, there will be something like 5,000 cells available
instead of just 50.
o This is why you can respond much more quickly to Ag the second time you encounter it.
o Recall the graph that displays Ab production for the adaptive immune response. The first time Ag is
encountered, Ab production is slow, perhaps 1-2 weeks. For the second encounter with the same Ag, the
response is much stronger and much faster.
o This is because you already have tons of B cells specific for that pathogen present so that the response is
quick, and expansion can ensue even further.
The B cell will eventually mature into a plasma cell.
o Ab factories: loaded with rough ER and ribosomes.
o They will migrate from the site where they were activated and go into the bone marrow (skull, sternum,
iliac crests)
 In someone with multiple myeloma, where plasma cells are growing uncontrollably, shadows can
be seen in the bone in x-ray. This is due to bone tissue death where the plasma cells were
growing uncontrollably.
T cells, depending on the pathogen and on the environment, will become either cytotoxic or helper T cells.
o Helper T cells will make cytokines to help eliminate invading pathogens by activating all the appropriate
cell types in the area.
Defects in the adaptive immune response
 Missing B cells or T cells; there are certain classic syndromes for that.
 T cells are missing in individuals that have DeGeorge’s syndrome.
o Because of developmental defects, they simply don’t have a thymus.
o They are severely immunocompromised as a result.
o They will have B cells and might even have reasonably normal Ig levels but won’t respond well to Ag
o They should not be vaccinated because they won’t be able to respond well to the vaccine.
 B cell defects where you don’t make Ab or don’t make B cells
 Severe combined immunodeficiencies, or SCIDs: you don’t have either B cells or T cells
o The only option is bone marrow transplantation.
o This is the “bubble boy” thing seen in movies or TV.
[End 48:21 mins]